npbhavya / Kraken2-output-manipulationLinks
Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each column is number of reads that were rooted to this taxon (column 2 in summary)
☆23Updated last year
Alternatives and similar repositories for Kraken2-output-manipulation
Users that are interested in Kraken2-output-manipulation are comparing it to the libraries listed below
Sorting:
- ☆83Updated last year
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆30Updated 5 years ago
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆45Updated last year
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆56Updated 3 years ago
- IS mapping software☆56Updated 3 years ago
- A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category☆70Updated 3 months ago
- Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.☆47Updated 4 months ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆135Updated 2 months ago
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆96Updated 4 months ago
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated 2 years ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆45Updated 2 years ago
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆124Updated last year
- A pipeline for running AMRfinderPlus and collating results into functional classes☆79Updated 11 months ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆145Updated 3 months ago
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆18Updated 5 years ago
- Nextflow pipeline to analyze PacBio HiFi full-length 16S data☆81Updated 3 weeks ago
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆41Updated 4 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆60Updated 5 months ago
- DDBJ Fast Annotation and Submission Tool☆81Updated 3 months ago
- Collection of scripts for bacterial genomics☆47Updated 5 years ago
- nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…☆70Updated 3 years ago
- Recovery of prokaryotic genomes from shotgun metagenomic sequencing data☆61Updated 4 years ago
- Reorients assembled microbial sequences☆124Updated 4 months ago
- MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.☆88Updated 11 months ago
- Sorts amplicons from Nanopore sequencing data based on similarity☆38Updated 2 months ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆137Updated last year
- A tool for drawing ANI clustermap between all-vs-all microbial genomes☆84Updated 3 months ago
- Adapter trimmer for Oxford Nanopore reads using ab initio method☆45Updated 8 months ago
- Horizontal gene transfer (HGT) identification pipeline☆61Updated 2 years ago